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Urbič T, Urbič T, Avbelj F, et al. Molecular Simulations Find Stable Structures in Fragments of Protein G. Acta Chim Slov. 2008;2008(55):385-395
Urbič, T., Urbič, T., Avbelj, F., & Dill, K. A. (2008). Molecular Simulations Find Stable Structures in Fragments of Protein G. Acta chimica Slovenica, 2008(55), 385-395.
Urbič, Tjaša, et al. "Molecular Simulations Find Stable Structures in Fragments of Protein G." Acta chimica Slovenica vol. 2008,55 (2008): 385-395.
Urbič T, Urbič T, Avbelj F, Dill KA. Molecular Simulations Find Stable Structures in Fragments of Protein G. Acta Chim Slov. 2008 Jan 26;2008(55):385-395. PMID: 20448839; PMCID: PMC2864544.
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Acta Chim Slov. 2008 Jan 26;2008(55):385-395.

Molecular Simulations Find Stable Structures in Fragments of Protein G.

Acta chimica Slovenica

Tjaša Urbič, Tomaž Urbič, Franc Avbelj, Ken A Dill

Affiliations

  1. National Institute of Chemistry Slovenia, Ljubljana, Slovenia.

PMID: 20448839 PMCID: PMC2864544

Abstract

We perform all-atom computer simulations on nearly one hundred 6-, 8-, 10-, and 12-mer peptide fragments of protein G, and look for stable states. We simulated by replica-exchange molecular dynamics using Amber7 with the parm96 force-field and a GB/SA (generalized-Born/solvent accessible) implicit solvent model. We find that useful diagnostics for identifying stable converged structures are the conformational entropy and free energy of each state. A large gap in the ground-state free-energy, and a low entropy indicate convergence to a single preferred peptide conformation. We find that a non-negligible fraction of such structures have some native-like character. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.

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